There is considerable interest in the role of selenium in cancer prevention. Various organic and inorganic Se compounds are considered to be antioxidants. In the present study, the binding modes, the binding constants and the stability of Se–DNA complexes have been determined by Fourier transform infrared (FTIR) and UV–Visible spectroscopic methods. Spectroscopic evidence showed that Na2SeO4 and Na2SeO3 bind to the minor and major grooves of DNA and the backbone phosphate (PO2) with overall binding constants of K(Na2SeO4–DNA) = 5.20 × 104 M−1 and K(Na2SeO3–DNA) = 1.87 × 103 M−1. DNA aggregations occurred at high selenium concentrations. No biopolymer conformational changes were observed upon Na2SeO3 and Na2SeO4 interactions, while DNA remained in the B-family structure.